Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain
Micronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm acc...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00213/full |
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| author | Haritha Bollinedi Ashutosh Kumar Yadav K. K. Vinod S. Gopala Krishnan Prolay Kumar Bhowmick M. Nagarajan C. N. Neeraja Ranjith Kumar Ellur Ashok Kumar Singh |
| author_facet | Haritha Bollinedi Ashutosh Kumar Yadav K. K. Vinod S. Gopala Krishnan Prolay Kumar Bhowmick M. Nagarajan C. N. Neeraja Ranjith Kumar Ellur Ashok Kumar Singh |
| author_sort | Haritha Bollinedi |
| collection | DOAJ |
| description | Micronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm accessions, grown at two locations, were evaluated for Fe and Zn in brown rice (BR) and milled rice (MR). A significant variation was observed in the rice germplasm for these micronutrients. The grain Fe concentration was in the range of 6.2–23.1 ppm in BR and 0.8–12.3 ppm in MR, while grain Zn concentration was found to be in the range of 11.0–47.0 ppm and 8.2–40.8 ppm in the BR and MR, respectively. Grain Fe exhibited maximum loss upon milling with a mean retention of 24.9% in MR, while Zn showed a greater mean retention of 74.2% in MR. A genome-wide association study (GWAS) was carried out implementing the FarmCPU model to control the population structure and kinship, and resulted in the identification of 29 marker-trait associations (MTAs) with significant associations for traits viz. FeBR (6 MTAs), FeMR (7 MTAs), ZnBR (11 MTAs), and ZnMR (5 MTAs), which could explain the phenotypic variance from 2.1 to as high as 53.3%. The MTAs governing the correlated traits showed co-localization, signifying the possibility of their simultaneous improvement. The robust MTAs identified in the study could be valuable resource for enhancing Fe and Zn concentration in the rice grain and addressing the problem of Fe and Zn malnutrition among rice consumers. |
| first_indexed | 2024-12-12T06:18:34Z |
| format | Article |
| id | doaj.art-537800b0cf2e444294909b97bf2621cf |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T06:18:34Z |
| publishDate | 2020-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-537800b0cf2e444294909b97bf2621cf2022-12-22T00:34:57ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-04-011110.3389/fgene.2020.00213497543Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice GrainHaritha Bollinedi0Ashutosh Kumar Yadav1K. K. Vinod2S. Gopala Krishnan3Prolay Kumar Bhowmick4M. Nagarajan5C. N. Neeraja6Ranjith Kumar Ellur7Ashok Kumar Singh8Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, IndiaICAR-Indian Institute of Rice Research, Hyderabad, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, IndiaMicronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm accessions, grown at two locations, were evaluated for Fe and Zn in brown rice (BR) and milled rice (MR). A significant variation was observed in the rice germplasm for these micronutrients. The grain Fe concentration was in the range of 6.2–23.1 ppm in BR and 0.8–12.3 ppm in MR, while grain Zn concentration was found to be in the range of 11.0–47.0 ppm and 8.2–40.8 ppm in the BR and MR, respectively. Grain Fe exhibited maximum loss upon milling with a mean retention of 24.9% in MR, while Zn showed a greater mean retention of 74.2% in MR. A genome-wide association study (GWAS) was carried out implementing the FarmCPU model to control the population structure and kinship, and resulted in the identification of 29 marker-trait associations (MTAs) with significant associations for traits viz. FeBR (6 MTAs), FeMR (7 MTAs), ZnBR (11 MTAs), and ZnMR (5 MTAs), which could explain the phenotypic variance from 2.1 to as high as 53.3%. The MTAs governing the correlated traits showed co-localization, signifying the possibility of their simultaneous improvement. The robust MTAs identified in the study could be valuable resource for enhancing Fe and Zn concentration in the rice grain and addressing the problem of Fe and Zn malnutrition among rice consumers.https://www.frontiersin.org/article/10.3389/fgene.2020.00213/fullFeZnbiofortificationGWASdonorsrice |
| spellingShingle | Haritha Bollinedi Ashutosh Kumar Yadav K. K. Vinod S. Gopala Krishnan Prolay Kumar Bhowmick M. Nagarajan C. N. Neeraja Ranjith Kumar Ellur Ashok Kumar Singh Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain Frontiers in Genetics Fe Zn biofortification GWAS donors rice |
| title | Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain |
| title_full | Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain |
| title_fullStr | Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain |
| title_full_unstemmed | Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain |
| title_short | Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain |
| title_sort | genome wide association study reveals novel marker trait associations mtas governing the localization of fe and zn in the rice grain |
| topic | Fe Zn biofortification GWAS donors rice |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00213/full |
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